Testing novel ideas about sequence change requires a mathematical representation with implementation in software. Most existing software packages for statistical analysis of comparative genomics are narrow in focus and not geared to the broader meta-data driven analyses of interest to us. Accordingly, we have developed the COmparative GENomics Toolkit (COGENT). This toolkit is the hub of our analytical activity, and is freely available. It provides facilities for genomic data manipulation, flexible model specification, and scales from single to multi-CPU architectures. A detailed description is available on our software page.
One project that aims to be generalised across biological processes concerns multiple alignment. This remains a significant challenge with most groups focussing on protein sequence alignments. We aim to develop a probabilistic multiple alignment approach that can incorporate insights from our analyses of genome mutation to improve fidelity. This project is being undertaken in collaboration with Cray Australia Pty. Ltd.